
Part B: Public Repositories
Pathway data
- WikiPathways
- Reactome
- KEGG
- Pathway Commons (collection)
- Published Pathway Figures
Network data
- STRING
- IntAct
- NDEx (collection)
Sources of PPI Data
- Experimental Techniques High Throughput Low
Throughput
- Computational Techniques
- Public Repositories
Know what to look for. Know what you’re getting.
Finding Network Data
Where do I find the network?
There is no such thing!
There are hundreds of different interaction databases 
It depends on your biological question and your analysis
plan,
But know what you are getting…..
Starting with a gene list……

Networks
Broad coverage / Lower resolution
- STRING (stringApp)
- NDEx (built-in)
- PSICQUIC (built-in)
- IntAct (IntAct App)
String
StringApp

STRING Settings

STRING Results

STRING Options

STRING Enrichment

NDEx
CyNDEx App
- Repository for biological network knowledge
- Organisations and individual scientists can deposit
- Use CyNDEx App to import/export networks
- Featured collections include:
- Pathway Interaction Database (NCI-PID)
- Cancer Cell Maps Initiative (CCMI)
- The NDEx Butler
- NetPath

PSICQUIC
PSI common query interface
PSICQUIC is included in the Cytoscape network search
tool:

IntAct
IntAct App


IntAct - Filters
- Can filter network by:
- MI Score
- Interaction detection method
- Participant detection method
- Host organism
- Expansion (e.g. spoke vs. matrix)
- Type (interaction type)
- Mutations (hides unmutated edges)
Pathways
Higher resolution / Limited coverage (~50% of genes)
- WikiPathways (WikiPathways App)
- Reactome (ReactomeFI App)
- Pathway Commons (CyPath2 App)
- KEGG (KEGGscape App)
WikiPathways
WikiPathways App
- Handmade pathway models
- Collaborative platform open to all researchers
- Thousands of pathways for dozens of species
Use the Network Search Tool to select a resource:

WikiPathways Search

WikiPathways Results

Pathway Database Apps

Cytoscape

Core Concepts

Cytoscape Apps!
apps.cytoscape.org

Loading Network Data
Cytoscape can import network data from:
- Files (or URLs)
- Excel, TSV, CSV
- XGMML: eXtensible Graph Markup and Modelling Language
- SBML: Systems Biology Markup Language
- BioPAX
- PSI-MI
- SIF: Simple Interaction Format
- GML: Graph Markup Language
- … and others depending on loaded Apps
Cytoscape can import network data from:
- Public repositories:
- PSICQUIC
- STRING (via the stringApp)
- IntAct (via the IntActApp)
- Reactome (via the ReactomeFI app)
- WikiPathways (via the WikiPathways app)
- Pathway Commons (via the CyPath2 app)
- NDEx
- Automation:
- Command line scripts
- CyREST via R, Python, etc
Cytoscape can load tables from:
- Files (or URLs)
- Public repositories
- Automation:
- Command line scripts
- CyREST via R, Python, etc
Saving and Exporting
- Sessions save everything as .cys files: Networks,
Tables, Styles, Screen sizes, etc.
- Export networks in different formats: SIF, GML, XGMML, BioPAX,
JSON
- Export tables as CSV files
- Publication quality graphics in several formats: PDF, SVG, PNG, and
JPEG
Tour of Cytoscape - Exercise
- Launch the latest version of Cytoscape

* Save your cytoscape app as a session in .cys
format for future use.
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